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Although evidence suggests that homocysteine levels are elevated in severe mental illness in children, findings regarding homocysteine levels in youth with anxiety and depression are scarce. Therefore, this study examined the association of homocysteine levels with anxiety and depression in a community sample of students aged 6-13 years. In total, 649 students were selected from the first, fourth, and seventh grades of schools in Taipei, Taiwan, in 2010. These students completed a hospital-based health examination, which included physical examination, blood sample collection, and questionnaire administration. The data were analysed through multiple linear regression. Among the seventh-grade boys, both depression (adjusted β = 0.044, 95% confidence interval (CI) = 0.004-0.084) and anxiety (adjusted β = 0.052, 95% CI = 0.013-0.091) were independently associated with increased homocysteine levels. In further dichotomisation, compared with students with low anxiety levels, those with moderate to high anxiety levels were significantly positively associated with elevated serum homocysteine levels (adjusted β = 0.091, 95% CI = 0.003-0.180). Our results suggest that increased depression and anxiety may be positively associated with higher serum homocysteine levels in older boys. Our results provide essential data on the biological aspects underlying anxiety and depression in the studied population.